@cpj3131 Depending on the tool you're using, some filters get applied that may modify what ends up getting counted.… https://t.co/yTGPKrsB9A

@cpj3131 It's a variant context annotation that counts the number of A, C, G, and T bases across all samples, in th… https://t.co/gVhAdpqOIv

Big day for #GATK users on AWS -- this means you can now run our #OpenWDL Best Practices workflows a lot more easil… https://t.co/y08881uLLv

Solutions to Problems

Tips for solving common problems and errors

Allele Depth (AD) is lower than expected
AnalyzeCovariates fails with error message "RScript exited with 1"
Errors about contigs in BAM or VCF files not being properly ordered or sorted
Errors about input files having missing or incompatible contigs
Errors about misencoded quality scores
Errors about read group (RG) information
Errors in SAM/BAM files can be diagnosed with ValidateSamFile
I am unable to use VQSR (recalibration) to filter variants
I do not get the annotations I specified with -A
I expect to see a variant at a specific site, but it's not getting called
I need to run programs that require different versions of Java